Reformatting through the System Setting will basically remove everything and keep your system hacked.
There is still currently to known method of restoring a NAND backup from one system to another without bricking the system. NANDs are encrypted to the system that backed them up. As well backing them up and restoring them still requires all of the SD content for the games to work. So you will need to make sure those are backed up as well.
So basically you need to whole damn SD card.

Reformatting through the System Setting will basically remove everything and keep your system hacked.
There is still currently to known method of restoring a NAND backup from one system to another without bricking the system. NANDs are encrypted to the system that backed them up. As well backing them up and restoring them still requires all of the SD content for the games to work. So you will need to make sure those are backed up as well.
So basically you need to whole damn SD card.

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Thanks! You pretty much answered everything I needed. Stinks about the complications of save backups. Guess I'll upload my Pokémon to poke bank and call it a day.

Once I restore through system setting everything hack wise will still be intact. CIAs will install still?